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Update Pipeline Configs #126

Update Pipeline Configs

Update Pipeline Configs #126

name: Update Pipeline Configs
on:
schedule:
- cron: "0 0 * * *" # Run every day at midnight
workflow_dispatch:
jobs:
update_configs:
runs-on: ubuntu-latest
steps:
- name: Checkout repository
uses: actions/checkout@v4
- name: Fetch pipeline names
run: |
curl -o pipeline_names.json https://nf-co.re/pipeline_names.json
- name: Check pipeline names and add missing configs
id: check-pipelines
run: |
pipeline=$(jq -r '.pipeline[]' pipeline_names.json)
for pipeline in $pipeline; do
printf "Checking pipeline: %s\n" $pipeline
if [ ! -f "pipeline/${pipeline}.config" ]; then
cat << EOF > "pipeline/${pipeline}.config"
/*
* -------------------------------------------------
* nfcore/${pipeline} custom profile Nextflow config file
* -------------------------------------------------
* Config options for custom environments.
* Cluster-specific config options should be saved
* in the conf/pipeline/${pipeline} folder and imported
* under a profile name here.
*/
profiles {
}
EOF
echo "changed=true" >> $GITHUB_OUTPUT
fi
done
- name: clean up
run: |
rm pipeline_names.json
- name: Commit & push changes
id: commit-and-push
if: steps.check-pipelines.outputs.changed == 'true'
run: |
git config user.email "[email protected]"
git config user.name "nf-core-bot"
git add .
git status
git commit -m "[automated] Update pipeline configs"
- name: Create PR
uses: peter-evans/create-pull-request@70a41aba780001da0a30141984ae2a0c95d8704e # v6
if: steps.check-pipelines.outputs.changed == 'true'
with:
token: ${{ secrets.GITHUB_TOKEN }}
commit-message: Update pipeline configs
title: Update pipeline configs
body: |
This is an automated PR to update pipeline configs for newly created nf-core pipelines.
branch: 'update-pipeline-configs-${{ github.run_id }}'
delete-branch: true
base: "master"
draft: false
reviewers: |
"mashehu"
"jfy133"
"maxulysse"